Phenotypic and genomic adaptations to the extremely high elevation in plateau zokor (Myospalax baileyi).

The evolutionary outcomes of high elevation adaptation have been extensively described. However, whether widely distributed high elevation endemic animals adopt uniform mechanisms during adaptation to different elevational environments remains unknown, especially with respect to extreme high elevation environments. To explore this, we analysed the phenotypic and genomic data of seven populations of plateau zokor (Myospalax baileyi) along elevations ranging from 2,700 to 4,300 m. Based on whole-genome sequencing data and demographic reconstruction of the evolutionary history, we show that two populations of plateau zokor living at elevations exceeding 3,700 m diverged from other populations nearly 10,000 years ago. Further, phenotypic comparisons reveal stress-dependent adaptation, as two populations living at elevations exceeding 3,700 m have elevated ratios of heart mass to body mass relative to other populations, and the highest population (4,300 m) displays alterations in erythrocytes. Correspondingly, genomic analysis of selective sweeps indicates that positive selection might contribute to the observed phenotypic alterations in these two extremely high elevation populations, with the adaptive cardiovascular phenotypes of both populations possibly evolving under the functional constrains of their common ancestral population. Taken together, phenotypic and genomic evidence demonstrates that heterogeneous stressors impact adaptations to extreme elevations and reveals stress-dependent and genetically constrained adaptation to hypoxia, collectively providing new insights into the high elevation adaptation.

Five new species of Eimeria Schneider, 1875 from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae: Caprinae) in the Hoh Xil Nature Reserve Area of Qinghai Province, China.

We examined faeces of 76 endangered Tibetan antelopes Pantholops hodgsonii (Abel) in May 2017, from the Hoh Xil Nature Reserve, Qinghai Province, China, and found 62/76 (82%) discharging oöcysts representing five new species of Eimeria Schneider, 1875. Oöcysts of Eimeria pantholopensis n. sp., found in 54/76 (71%) chiru, are subspheroidal/ellipsoidal, 15-22 × 12-19 (18.6 × 16.1) µm, with a length/width (L/W) ratio of 1.0-1.3 (1.2); micropyle cap and 1-3 polar granules are present, but oöcyst residuum is absent. Sporocysts are ovoidal, 7-11 × 4-6 (9.2 × 5.3) µm, with a L/W ratio of 1.6-2.0 (1.7); Stieda body and sporocyst residuum of small, scattered granules are present; each sporozoite contains 2 refractile bodies. Oöcysts of Eimeria wudaoliangensis n. sp. found in 52/76 (68%) chiru, are pyriform, 21-29 × 17-21 (24.9 × 19.0) µm, with a L/W ratio of 1.1-1.5 (1.3); micropyle, micropyle cap and 1-4 polar granules are present, but oöcyst residuum is absent. Sporocysts are ovoidal, 9-13 × 5-8 (11.7 × 6.7) µm, with a L/W ratio of 1.4-2.7 (1.7); Stieda body and sporocyst residuum of disbursed granules are present; sporozoites have a single large refractile body. Oöcysts of Eimeria hodgsonii n. sp. found in 20/76 (26%) chiru, are elongate-ellipsoidal, 25-32 × 18-21 (28.9 × 19.8) µm, with a L/W ratio of 1.2-1.7 (1.5); micropyle, micropyle cap and 1-3 polar granules are present, but oöcyst residuum is absent. Sporocysts are ovoidal, 11-14 × 6-7 (12.3 × 6.8) µm, with a L/W ratio of 1.7-2.1 (1.8); Stieda body and sporocyst residuum as group of large granules lying along the interface between intertwined sporozoites are present; sporozoites have 2 refractile bodies. Oöcysts of Eimeria schalleri n. sp. found in 49/76 (64.5%) chiru, are ellipsoidal, 26-36 × 19-25 (30.4 × 23.2) µm, with a L/W ratio of 1.2-1.5 (1.3); micropyle with micropyle cap and polar granules appearing as many diffuse tiny bodies are present, but oöcyst residuum is absent. Sporocysts are ovoidal, 12-16 × 7-9 (14.2 × 7.8) µm, with a L/W ratio of 1.6-2.1 (1.8); Stieda body and sporocyst residuum are present, the latter as a group of small dispersed granules between intertwined sporozoites; sporozoites with 2 refractile bodies. Oöcysts of Eimeria sui n. sp. found in 4/76 (5%) chiru, are ovoidal, 32-38 × 26-30 (36.6 × 28.6) µm, with a L/W ratio of 1.0-1.4 (1.3); micropyle and micropyle cap and 1-3 polar granules are present, but oöcyst residuum is absent. Sporocysts are ovoidal, 15-18 × 8-10 (16.7 × 8.9) µm, with a L/W ratio of 1.7-2.1 (1.9); Stieda body and sporocyst residuum are present, the latter as a group of dispersed small granules; sporozoites with 2 refractile bodies. Five of 62 faecal samples in which oöcysts were detected (8%) had a single species infection, 13 of 62 (21%) had two species, 28 of 62 (45%) had three species and 16 of 62 (26%) had four species.

The complete mitochondrial DNA sequence of the Chinese red pika (Ochotona erythrotis).

In this study, we undertook the first complete Ochotona erythrotis mitochondrial genome. The genome sequence was 16,663 bp in length, including the typical structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and the non-coding control region. The overall base composition of O. erythrotis mitogenome is 31.8% A, 26.0% T, 28.6% G, and 13.6% C, with a high A + T content of 57.8%.

[Molecular authentication of Sailonggu and its resource distribution in Qinghai-Tibet Plateau].

To provide accurate information on geographic distribution of crude drug Sailonggu in the plateau, we identified zokor species (Eospalax spp.) in Qinghai-Tibet Plateau using molecular methods. Based on the mitochondrial cytochrome B (cytb) gene sequences, we then extracted haplotypes from these sequences and reconstructed phylogenetic trees for the haplotypes using both maximum likelihood (ML) and Bayesian inference (BI) methods. Based on the trees, the species of each sample were determined. Five hundred and three samples from 35 populations were sequenced and their whole cytb sequences (1140 bp) were obtained. From these sequences 150 haplotypes were detected, in which, 126 were Eospalax baileyi, 20 were E. cansus, and 4 were E. smithi of the 35 populations, 28 were E. baileyi type, 5 were E. cansus type, and the remaining 2 were mixed of E. baileyi + E. cansus (DT2) and E. baileyi + E. smithi (ZN3). The results showed that, the regions around the Qinghai lake and near the upper stream of Yellow River started at Guide could be viewed as the producing area of authentic Sailonggu, and also, the cytb gene is a powerful molecular marker to determine the species of zokors as well as for the authentication of geographic distribution of Sailonggu.

Molecular identification of Taenia mustelae cysts in subterranean rodent plateau zokors (Eospalax baileyi).

Cestode larvae spend one phase of their two-phase life cycle in the viscera of rodents, but cases of cestodes infecting subterranean rodents have only been rarely observed. To experimentally gain some insight into this phenomenon, we captured approximately 300 plateau zokors (Eospalax baileyi), a typical subterranean rodent inhabiting the Qinghai-Tibet Plateau, and examined their livers for the presence of cysts. Totally, we collected five cysts, and using a mitochondrial gene (cox1) and two nuclear genes (pepck and pold) as genetic markers, we were able to analyze the taxonomy of the cysts. Both the maximum likelihood and Bayesian methods showed that the cysts share a monophyly with Taenia mustelae, while Kimura 2-parameter distances and number of different sites between our sequences and T. mustelae were far less than those found between the examined sequences and other Taeniidae species. These results, alongside supporting paraffin section histology, imply that the cysts found in plateau zokors can be regarded as larvae of T. mustelae, illustrating that zokors are a newly discovered intermediate host record of this parasite.

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia).

BACKGROUND: Subterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground. Owing to the convergence of morphological traits and the incongruence of molecular evidence, the phylogenetic relationships among three subfamilies Myospalacinae (zokors), Spalacinae (blind mole rats) and Rhizomyinae (bamboo rats) within the family Spalacidae remain unresolved. Here, we performed de novo transcriptome sequencing of four RNA-seq libraries prepared from brain and liver tissues of a plateau zokor (Eospalax baileyi) and a hoary bamboo rat (Rhizomys pruinosus), and analyzed the transcriptome sequences alongside a published transcriptome of the Middle East blind mole rat (Spalax galili). We characterize the transcriptome assemblies of the two spalacids, and recover the phylogeny of the three subfamilies using a phylogenomic approach. RESULTS: Approximately 50.3 million clean reads from the zokor and 140.8 million clean reads from the bamboo ratwere generated by Illumina paired-end RNA-seq technology. All clean reads were assembled into 138,872 (the zokor) and 157,167 (the bamboo rat) unigenes, which were annotated by the public databases: the Swiss-prot, Trembl, NCBI non-redundant protein (NR), NCBI nucleotide sequence (NT), Gene Ontology (GO), Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 5,116 nuclear orthologous genes were identified in the three spalacids and mouse, which was used as an outgroup. Phylogenetic analysis revealed a sister group relationship between the zokor and the bamboo rat, which is supported by the majority of gene trees inferred from individual orthologous genes, suggesting subfamily Myospalacinae is more closely related to subfamily Rhizomyinae. The same topology was recovered from concatenated sequences of 5,116 nuclear genes, fourfold degenerate sites of the 5,116 nuclear genes and concatenated sequences of 13 protein coding mitochondrial genes. CONCLUSIONS: This is the first report of transcriptome sequencing in zokors and bamboo rats, representing a valuable resource for future studies of comparative genomics in subterranean mammals. Phylogenomic analysis provides a conclusive resolution of interrelationships of the three subfamilies within the family Spalacidae, and highlights the power of phylogenomic approach to dissect the evolutionary history of rapid radiations in the tree of life.

Four new coccidia (Apicomplexa: Eimeriidae) from the Plateau zokor, Myospalax baileyi Thomas (Rodentia: Myospalacinae), a subterranean rodent from Haibei area, Qinghai Province, China.

Thirty-eight faecal samples from the Plateau zokor, Myospalax baileyi Thomas, collected in the Haibei Area, Qinghai Province, China, were examined for the presence of coccidia (Apicomplexa: Eimeriidae). Seventeen of 38 faecal samples (44.7%) were found to contain coccidian oöcysts representing four new species of Eimeria Schneider, 1875, and four of 17 (23.5%) infected zokors were concurrently infected with two or three of these eimerian species. The sporulated oöcysts of Eimeria myospalacensis n. sp. are ovoidal, 9.5-17.0 × 8.0-13.0 (mean 13.0 × 10.4) µm; a polar granule is present, oöcyst residuum is absent; sporocysts are ovoidal, 4.5-7.5 × 3.0-5.0 (mean 6.3 × 4.2) µm and have both a Stieda body and residuum. Oöcysts of Eimeria fani n. sp. are ellipsoidal to cylindroidal, 12.5-16.0 × 8.0-11.0 (mean 14.6 × 9.9) µm; a polar granule is present, but micropyle and residuum are lacking; sporocysts are ovoidal, 4.5-7.5 × 3.0-5.3 (mean 6.7 × 4.4) µm; a residuum and a Steida body are present. Oöcysts of Eimeria baileyii n. sp. are ellipsoidal, 15.0-23.0 × 12.0-18.0 (mean 18.2 × 13.7) µm; a polar granule is present but oöcyst residuum is absent; sporocysts are ovoidal, 8.0-11.0 × 5.0-7.0 (mean 9.5 × 5.9) µm and have both a Stieda body and residuum. Oöcysts of Eimeria menyuanensis n. sp. are ovoidal, 12.5-21.0 × 11.0-18.0 (mean 17.1 × 14.6) µm, with a distinct micropyle c.2.5 µm wide; a polar granule is present but a residuum is absent; sporocysts are ovoidal, 8.0-12.0 × 5.0-7.0 (mean 10.2 × 6.4) µm, and have both a Stieda body and residuum.

Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals.

Hibernating mammals need to be insensitive to acid in order to cope with conditions of high CO2; however, the molecular basis of acid tolerance remains largely unknown. The African naked mole-rat (Heterocephalus glaber) and hibernating mammals share similar environments and physiological features. In the naked mole-rat, acid insensitivity has been shown to be conferred by the functional motif of the sodium ion channel NaV1.7. There is now an opportunity to evaluate acid insensitivity in other taxa. In this study, we tested for functional convergence of NaV1.7 in 71 species of mammals, including 22 species that hibernate. Our analyses revealed a functional convergence of amino acid sequences, which occurred at least six times independently in mammals that hibernate. Evolutionary analyses determined that the convergence results from both parallel and divergent evolution of residues in the functional motif. Our findings not only identify the functional molecules responsible for acid insensitivity in hibernating mammals, but also open new avenues to elucidate the molecular underpinnings of acid insensitivity in mammals.